Fig. 4

ADNP methylation signature in the juvenile post-mortem cerebellum. (A) Genomic scatter plot indicating the hypermethylated genes (Δβ > 0.2) of the patient (red), the hypomethylated genes (Δβ < −0.2) of the patient (blue). The chromosomal positions of the genes are shown on the x-axis. (B) Pyrosequencing confirmation of a subset of hyper- and hypomethylated genes. Hypermethylated genes, e.g., OTX2, SLC25A21 and DNAJ6, show increased CpG methylation in the patient, whereas hypomethylated genes, e.g., COL4A2, MAGI2 and CTNND2, present with a nearly absent percentage of CpG methylation. (C) Metascape functional annotation of biological processes. Hyper- and hypomethylated genes cluster in associated processes such as the actin cytoskeleton and nervous system developmental disorder amongst others. (D) Predictive String v11.5 protein–protein interaction analysis of ADNP. The proteins are indicated as nodes with interconnecting lines representing the interaction. ADNP is surrounded by protein regulating specific autophagy-related processes and protein ubiquitination. (E) Transcription factors (TFs) enriched in patient cerebellum of hyper- and hypomethylated gene co-expression. TFs associated with hypermethylated genes are represented in blue, while the TFs associated with the hypomethylated genes are depicted in red. TFs shared amongst the overlapping genes are shown in green. ADNP was identified as the top transcription factor controlling the hypomethylated genes (black box)